Identifying the ‘unidentified’ fungi: a global-scale long-read third-generation sequencing approach

Regional-Scale In-Depth Analysis of Soil Fungal Diversity Reveals Strong pH and Plant Species Effects in Northern Europe

(2020) Leho Tedersoo et al.   Frontiers in Microbiology

Fungi in aquatic ecosystems

(2019) Hans-Peter Grossart et al.   NATURE REVIEWS MICROBIOLOGY

Megaphylogeny resolves global patterns of mushroom evolution

(2019) Torda Varga et al.   Nature Ecology & Evolution

A few Ascomycota taxa dominate soil fungal communities worldwide

(2019) Eleonora Egidi et al.   Nature Communications

Towards PacBio‐based pan‐eukaryote metabarcoding using full‐length ITS sequences

(2019) Leho Tedersoo et al.   Environmental Microbiology Reports

Host availability drives distributions of fungal endophytes in the imperilled boreal realm

(2019) Jana M. U’Ren et al.   Nature Ecology & Evolution

Relative Performance of MinION (Oxford Nanopore Technologies) versus Sequel (Pacific Biosciences) Third-Generation Sequencing Instruments in Identification of Agricultural and Forest Fungal Pathogens

(2019) Kaire Loit et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

High-level classification of the Fungi and a tool for evolutionary ecological analyses

(2018) Leho Tedersoo et al.   FUNGAL DIVERSITY

Microbial island biogeography: isolation shapes the life history characteristics but not diversity of root-symbiotic fungal communities

(2018) John Davison et al.   ISME Journal

Clarifying the Relationships between Microsporidia and Cryptomycota

(2018) David Bass et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Long-read DNA metabarcoding of ribosomal RNA in the analysis of fungi from aquatic environments

(2018) Felix Heeger et al.   Molecular Ecology Resources

Introducing ribosomal tandem repeat barcoding for fungi

(2018) Christian Wurzbacher et al.   Molecular Ecology Resources

Mycobiome diversity: high-throughput sequencing and identification of fungi

(2018) R. Henrik Nilsson et al.   NATURE REVIEWS MICROBIOLOGY

Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota

(2018) Ying Chang et al.   NEW PHYTOLOGIST

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

(2018) Rolf Henrik Nilsson et al.   NUCLEIC ACIDS RESEARCH

Filling gaps in the microsporidian tree: rDNA phylogeny of Chytridiopsis typographi (Microsporidia: Chytridiopsida)

(2018) Daniele Corsaro et al.   PARASITOLOGY RESEARCH

Leveraging single-cell genomics to expand the fungal tree of life

(2018) Steven R. Ahrendt et al.   Nature Microbiology

PipeCraft: Flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data

(2017) Sten Anslan et al.   Molecular Ecology Resources

Glomeromycotina: what is a species and why should we care?

(2017) Thomas D. Bruns et al.   NEW PHYTOLOGIST

PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives

(2017) Leho Tedersoo et al.   NEW PHYTOLOGIST

Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes

(2017) Sebastien Colin et al.   eLife

Novel soil-inhabiting clades fill gaps in the fungal tree of life

(2017) Leho Tedersoo et al.   Microbiome

Multigene phylogeny of Endogonales, an early diverging lineage of fungi associated with plants

(2017) Alessandro Desirò et al.   IMA Fungus

A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data

(2016) Joseph W. Spatafora et al.   MYCOLOGIA

Digital identifiers for fungal species

(2016) U. Kõljalg et al.   SCIENCE

Fungal identification biases in microbiome projects

(2016) Leho Tedersoo et al.   Environmental Microbiology Reports

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Top 50 most wanted fungi

(2016) R. Henrik Nilsson et al.   MycoKeys

Response to Comment on "Global diversity and geography of soil fungi"

(2015) L. Tedersoo et al.   SCIENCE

Towards an integrated phylogenetic classification of the Tremellomycetes

(2015) X.-Z. Liu et al.   STUDIES IN MYCOLOGY

Entorrhizomycota: A New Fungal Phylum Reveals New Perspectives on the Evolution of Fungi

(2015) Robert Bauer et al.   PLoS One

Global diversity and geography of soil fungi

(2014) L. Tedersoo et al.   SCIENCE

A first comprehensive census of fungi in soil reveals both hyperdiversity and fine-scale niche partitioning

(2013) D. Lee Taylor et al.   ECOLOGICAL MONOGRAPHS

Microsporidian Diversity in Soil, Sand, and Compost of the Pacific Northwest

(2013) Alex M. Ardila-Garcia et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Towards a unified paradigm for sequence-based identification of fungi

(2013) Urmas Kõljalg et al.   MOLECULAR ECOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Fungi: 1, 2, 3 … 5.1 million species?

(2011) Meredith Blackwell   AMERICAN JOURNAL OF BOTANY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Exploring and quantifying fungal diversity in freshwater lake ecosystems using rDNA cloning/sequencing and SSU tag pyrosequencing

(2011) Sébastien Monchy et al.   ENVIRONMENTAL MICROBIOLOGY

From morphology to molecular biology: can we use sequence data to identify fungal endophytes?

(2011) Thida Win Ko Ko et al.   FUNGAL DIVERSITY

Discovery of novel intermediate forms redefines the fungal tree of life

(2011) Meredith D. M. Jones et al.   NATURE

Where is the unseen fungal diversity hidden? A study of Mortierella reveals a large contribution of reference collections to the identification of fungal environmental sequences

(2011) László G. Nagy et al.   NEW PHYTOLOGIST

The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota)

(2010) M. Öpik et al.   NEW PHYTOLOGIST

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS